Load packages, functions, paths

library(dplyr)
## 
## Attaching package: 'dplyr'
## 
## The following objects are masked from 'package:stats':
## 
##     filter, lag
## 
## The following objects are masked from 'package:base':
## 
##     intersect, setdiff, setequal, union
library(tidyr)
library(ggplot2)
## Warning: package 'ggplot2' was built under R version 3.2.3
library(calibrate)
## Loading required package: MASS
## Warning: package 'MASS' was built under R version 3.2.2
## 
## Attaching package: 'MASS'
## 
## The following object is masked from 'package:dplyr':
## 
##     select
library(knitr)
"%&%" = function(a,b) paste(a,b,sep="")
my.dir = "/Volumes/dolan-lab/hwheeler/ThePlatinumStudy/GWAS/"
res.dir <- my.dir %&% "genotypes/UMich_imputation_results/PrediXcan/PrediXcan_results/"
source(my.dir %&% "genotypes/qqunif_px.r")
source(my.dir %&% "manhattan.R")

rnGM412 = pred_exp + ageaudio + CumlCispdose + 10 PCs

Bonf. sig. tissues:

  • TW_Brain-FrontalCortex-BA9_ElasticNet.0.5
  • TW_Esophagus-GastroesophagealJunction_ElasticNet.0.5
  • TW_Lung_ElasticNet.0.5
  • nearly sig. TW_Pituitary_ElasticNet.0.5
tislist <- scan(my.dir %&% "pred_exp_list","c")
wfs1res <- data.frame()
for(tis in tislist){
  res = read.table(res.dir %&% "N88_n953_rnGM412_ageaudio.cisp.10PCs_" %&% tis %&% ".linreg.PrediXcan",header=T)
  newres = mutate(res,CHR=as.numeric(gsub("chr","",chr)),BP=start,SNP=gene) %>% arrange(CHR,BP)
  res <- newres[complete.cases(newres),] #rm NAs
  wfs1res <- rbind(wfs1res,filter(res,gene=="WFS1") %>% mutate(tissue=tis))
  if(min(res$P)<0.0001){
    manhattan(res,suggestiveline=FALSE,genomewideline = -log10(0.05/dim(res)[1]),main="rnGM412 " %&% tis,annotatePval = 0.0001,cex.main=0.8)
    tophits <- dplyr::filter(res,P<=0.0001) %>% arrange(P) %>% dplyr::select(-CHR,-BP,-SNP)
    cat('\n')
    print(kable(tophits))
    cat('\n')
  }
  else{
    manhattan(res,suggestiveline=FALSE,genomewideline = -log10(0.05/dim(res)[1]),main="rnGM412 " %&% tis,cex.main=0.8)
    cat('\n')
  }
  qq<-qqunif(res$P,plot=TRUE,title="rnGM412 " %&% tis)
  cat('\n')
}

Estimate SE t.value P n gene chr strand start end ensid
17.88092 4.524379 3.952127 8.87e-05 512 DHCR7 chr11 - 71139239 71163914 ENSG00000172893.11

Estimate SE t.value P n ensid chr strand start end gene
2.941206 0.7072352 4.158738 3.77e-05 512 ENSG00000185873.7 chr4 - 69092371 69111438 TMPRSS11B

Estimate SE t.value P n ensid chr strand start end gene
1.449134 0.3548323 4.083996 5.16e-05 512 ENSG00000204779.2 chr9 - 70175707 70178815 FOXD4L5

Estimate SE t.value P n ensid chr strand start end gene
0.7657044 0.1926116 3.975381 8.07e-05 512 ENSG00000258231.1 chr12 + 58937907 59206842 RP11-362K2.2

Estimate SE t.value P n ensid chr strand start end gene
2.784477 0.6037721 4.611801 5.1e-06 512 ENSG00000198765.7 chr1 + 115397424 115537991 SYCP1
-1.191856 0.2631764 -4.528736 7.4e-06 512 ENSG00000140993.6 chr16 - 3353759 3355150 TIGD7

Estimate SE t.value P n ensid chr strand start end gene
1.128057 0.2791737 4.040698 6.17e-05 512 ENSG00000126785.8 chr14 + 63670832 63759937 RHOJ

Estimate SE t.value P n ensid chr strand start end gene
-0.8323534 0.2112283 -3.94054 9.29e-05 512 ENSG00000159023.14 chr1 + 29213603 29442315 EPB41

Estimate SE t.value P n ensid chr strand start end gene
-1.727885 0.4036983 -4.28014 2.24e-05 512 ENSG00000266173.1 chr17 - 61787851 61819330 STRADA

Estimate SE t.value P n ensid chr strand start end gene
0.3131696 0.0795167 3.938414 9.37e-05 512 ENSG00000157259.6 chr7 + 92076767 92088150 GATAD1

Estimate SE t.value P n ensid chr strand start end gene
-8.188064 1.7716557 -4.621702 4.90e-06 512 ENSG00000152518.5 chr2 - 43449541 43453748 ZFP36L2
1.141962 0.2514928 4.540734 7.00e-06 512 ENSG00000081041.8 chr4 - 74962752 74965010 CXCL2
-1.360753 0.3217150 -4.229683 2.79e-05 512 ENSG00000103449.7 chr16 - 51169886 51185278 SALL1

Estimate SE t.value P n ensid chr strand start end gene
2.31032 0.5339844 4.326569 1.83e-05 512 ENSG00000166685.7 chr17 + 71189129 71203047 COG1

Estimate SE t.value P n ensid chr strand start end gene
-1.277628 0.3033912 -4.211159 3.02e-05 512 ENSG00000163898.5 chr3 - 185224050 185270401 LIPH

Estimate SE t.value P n ensid chr strand start end gene
-0.5075917 0.1239854 -4.093964 4.95e-05 512 ENSG00000163297.12 chr4 - 80822303 81046608 ANTXR2

Estimate SE t.value P n ensid chr strand start end gene
-1.877541 0.3319178 -5.656644 0 512 ENSG00000196228.2 chr2 + 108863651 108881807 SULT1C3

Estimate SE t.value P n ensid chr strand start end gene
3.010339 0.6883930 4.372995 1.49e-05 512 ENSG00000168484.8 chr8 + 22016126 22021992 SFTPC
-0.658866 0.1666127 -3.954477 8.78e-05 512 ENSG00000184608.4 chr8 + 11225911 11296167 C8orf12

Estimate SE t.value P n ensid chr strand start end gene
17.24085 4.292209 4.016779 6.81e-05 512 ENSG00000185818.7 chr4 + 2061239 2070816 NAT8L

Estimate SE t.value P n ensid chr strand start end gene
11.8865245 2.8499725 4.170751 3.58e-05 512 ENSG00000144228.4 chr2 + 139259371 139331117 SPOPL
1.0510598 0.2532427 4.150404 3.90e-05 512 ENSG00000118402.5 chr6 - 80624529 80657297 ELOVL4
1.5094305 0.3666612 4.116690 4.50e-05 512 ENSG00000066336.7 chr11 - 47376411 47400127 SPI1
0.8091094 0.2009450 4.026522 6.54e-05 512 ENSG00000180488.10 chr1 + 78245309 78344106 FAM73A
3.0919529 0.7708814 4.010932 6.98e-05 512 ENSG00000166173.9 chr15 - 71123863 71146498 LARP6
-2.9586827 0.7522423 -3.933151 9.57e-05 512 ENSG00000099338.18 chr19 + 38826415 38861589 CATSPERG

Estimate SE t.value P n ensid chr strand start end gene
0.518625 0.1273885 4.071207 5.44e-05 512 ENSG00000204305.9 chr6 - 32148745 32150978 AGER
-6.619389 1.6485619 -4.015250 6.85e-05 512 ENSG00000185873.7 chr4 - 69092371 69111438 TMPRSS11B

Estimate SE t.value P n ensid chr strand start end gene
0.7297674 0.1728359 4.222313 2.88e-05 512 ENSG00000103091.10 chr16 - 74907468 75031071 WDR59
-1.6279861 0.4099694 -3.970995 8.21e-05 512 ENSG00000168298.4 chr6 + 26156559 26157343 HIST1H1E

Estimate SE t.value P n ensid chr strand start end gene
1.624558 0.4008128 4.053159 5.86e-05 512 ENSG00000123444.9 chr11 - 47597118 47597251 KBTBD4

Estimate SE t.value P n ensid chr strand start end gene
4.0381296 0.9686581 4.168787 3.61e-05 512 ENSG00000083799.13 chr16 + 50775961 50835846 CYLD
-0.6462027 0.1635625 -3.950800 8.91e-05 512 ENSG00000160200.13 chr21 - 44473301 44497053 CBS

WFS1 PrediXcan results

kable(dplyr::select(wfs1res,-CHR,-BP,-SNP))
Estimate SE t.value P n gene chr strand start end ensid tissue
-0.2555898 0.2242715 -1.1396448 0.2549821 512 WFS1 chr4 + 6271576 6304992 ENSG00000109501.9 DGN-WB
-2.5065203 0.8537576 -2.9358689 0.0034799 512 WFS1 chr4 + 6271576 6304992 ENSG00000109501.9 TW_Adipose-Subcutaneous_ElasticNet.0.5
-2.8904565 0.8928050 -3.2375003 0.0012862 512 WFS1 chr4 + 6271576 6304992 ENSG00000109501.9 TW_AdrenalGland_ElasticNet.0.5
0.0542483 0.2206135 0.2458975 0.8058629 512 WFS1 chr4 + 6271576 6304992 ENSG00000109501.9 TW_Artery-Coronary_ElasticNet.0.5
-0.2435284 0.4313156 -0.5646176 0.5725881 512 WFS1 chr4 + 6271576 6304992 ENSG00000109501.9 TW_Artery-Tibial_ElasticNet.0.5
-0.1057435 0.0505794 -2.0906435 0.0370664 512 WFS1 chr4 + 6271576 6304992 ENSG00000109501.9 TW_Brain-CerebellarHemisphere_ElasticNet.0.5
-0.1718972 0.0695706 -2.4708299 0.0138137 512 WFS1 chr4 + 6271576 6304992 ENSG00000109501.9 TW_Brain-Cerebellum_ElasticNet.0.5
-0.5634426 0.9920715 -0.5679456 0.5703279 512 WFS1 chr4 + 6271576 6304992 ENSG00000109501.9 TW_Brain-Hypothalamus_ElasticNet.0.5
-0.2751333 0.2536470 -1.0847092 0.2785753 512 WFS1 chr4 + 6271576 6304992 ENSG00000109501.9 TW_Heart-AtrialAppendage_ElasticNet.0.5
0.0431550 0.4187138 0.1030656 0.9179524 512 WFS1 chr4 + 6271576 6304992 ENSG00000109501.9 TW_Liver_ElasticNet.0.5
-0.2954065 0.1133866 -2.6053046 0.0094539 512 WFS1 chr4 + 6271576 6304992 ENSG00000109501.9 TW_Muscle-Skeletal_ElasticNet.0.5
-0.6493673 0.2658083 -2.4429908 0.0149125 512 WFS1 chr4 + 6271576 6304992 ENSG00000109501.9 TW_Nerve-Tibial_ElasticNet.0.5
-0.0837388 0.0759499 -1.1025534 0.2707537 512 WFS1 chr4 + 6271576 6304992 ENSG00000109501.9 TW_Skin-NotSunExposed-Suprapubic_ElasticNet.0.5
-0.1868429 0.0828212 -2.2559797 0.0245049 512 WFS1 chr4 + 6271576 6304992 ENSG00000109501.9 TW_Skin-SunExposed-Lowerleg_ElasticNet.0.5
0.0283218 0.1402027 0.2020060 0.8399945 512 WFS1 chr4 + 6271576 6304992 ENSG00000109501.9 TW_Spleen_ElasticNet.0.5
-0.5249366 0.1942954 -2.7017451 0.0071329 512 WFS1 chr4 + 6271576 6304992 ENSG00000109501.9 TW_Thyroid_ElasticNet.0.5